On 04/04/2023 08:07, Mark Saper wrote:
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Dear Paul,
I’ve discovered a serious problem when running Coot 0.9.7 from CCP4-8.0 (macOS
13.3). The problem is in the menu commands Real Space Refine Zone or
Regularize. If I select a zone comprised of 3 consecutive DNA nucleotides which
are in decent density, the refinement fails as in the first attached figure.
Often the DNA takes on random conformations.
If I repeat the same test with the same coordinates, map, and 3 nucleotides,
using Coot 0.9.6 from CCP4-7.1, the refinement is successful and results in the
second attached figure.
I think the same problem occurs with some polypeptide chains.
Hello Mark,
If you are accurately reporting the version numbers then I believe that
this issue may have been fixed in 0.9.8.7. Here are the release notes
Release 0.9.8.7
o FEATURE: res_tracer() added to the API
o FEATURE: read_mtz() added to the API [ChatGPT guessed at this
function name, and there is
no reason for it not to be there]
o BUG-FIX: PDBe URLs fixed for downloading dictionaries with pyrogen
o BUG-FIX: Carbohydrate Linking fixed again [Keitaro Yamashita and
others]
o BUG-FIX: RNA linking fixed [Keitaro Yamashita and Andrey Lebadev]
o NOTE: Coot is now tested against the new monomer library.
Paul.
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